The genome of the marine medaka Oryzias melastigma

Hui Su Kim; Bo Young Lee; Jeonghoon Han; Chang Bum Jeong; Dae Sik Hwang; Min Chul Lee; Hye Min Kang; Duck Hyun Kim; Daehwan Lee; Jaebum Kim; Ik Young Choi; Jae Seong Lee

doi:10.1111/1755-0998.12769

The genome of the marine medaka Oryzias melastigma

Hui Su Kim, Bo Young Lee, Jeonghoon Han, Chang Bum Jeong, Dae Sik Hwang, Min Chul Lee, Hye Min Kang, Duck Hyun Kim, Daehwan Lee, Jaebum Kim, Ik Young Choi, Jae Seong Lee

Department of Biological Sciences

Research output: Contribution to journal › Article › peer-review

38 Scopus citations

Abstract

Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field-based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole-genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50 = 23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish and zebrafish) were identified. Genome analyses revealed that the O. melastigma genome is highly heterozygous and contains a large number of repeat sequences. This assembly represents a useful genomic resource for fish scientists.

Original language	English
Pages (from-to)	656-665
Number of pages	10
Journal	Molecular Ecology Resources
Volume	18
Issue number	3
DOIs	https://doi.org/10.1111/1755-0998.12769
State	Published - May 2018

Keywords

genome assembly
marine medaka
Oryzias melastigma
RACA

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10.1111/1755-0998.12769

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title = "The genome of the marine medaka Oryzias melastigma",

abstract = "Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field-based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole-genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50 = 23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish and zebrafish) were identified. Genome analyses revealed that the O. melastigma genome is highly heterozygous and contains a large number of repeat sequences. This assembly represents a useful genomic resource for fish scientists.",

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year = "2018",

month = may,

doi = "10.1111/1755-0998.12769",

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AU - Kim, Hui Su

AU - Lee, Bo Young

AU - Han, Jeonghoon

AU - Jeong, Chang Bum

AU - Hwang, Dae Sik

AU - Lee, Min Chul

AU - Kang, Hye Min

AU - Kim, Duck Hyun

AU - Lee, Daehwan

AU - Kim, Jaebum

AU - Choi, Ik Young

AU - Lee, Jae Seong

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AB - Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field-based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole-genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50 = 23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish and zebrafish) were identified. Genome analyses revealed that the O. melastigma genome is highly heterozygous and contains a large number of repeat sequences. This assembly represents a useful genomic resource for fish scientists.

KW - genome assembly

KW - marine medaka

KW - Oryzias melastigma

KW - RACA

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The genome of the marine medaka Oryzias melastigma

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Keywords

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